diff --git a/README.md b/README.md index 70999fcbd45def49287220fa9dff9cfca0f76f4a..8e2207df5183f13149e7b34f60f3c573a82f2d61 100644 --- a/README.md +++ b/README.md @@ -196,6 +196,11 @@ Hub-CDB and Institut Pasteur <br /><br /> ## WHAT'S NEW IN +### v14.8.0 + +1) Small bug fixed for B.1.525 in voc.txt + + ### v14.7.0 1) B.1.620 added diff --git a/dataset/20210430_Variants of concern.xlsx b/dataset/20210430_Variants of concern.xlsx deleted file mode 100644 index 834052617140b85b67ef2230edfca36cac58164f..0000000000000000000000000000000000000000 Binary files a/dataset/20210430_Variants of concern.xlsx and /dev/null differ diff --git a/dataset/20210517_Variants of concern.xlsx b/dataset/20210517_Variants of concern.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..06d08d71a64e4d9db79d44b49e612e8b88a9593b Binary files /dev/null and b/dataset/20210517_Variants of concern.xlsx differ diff --git a/dataset/20210511_voc.gmt b/dataset/20210517_voc.gmt similarity index 97% rename from dataset/20210511_voc.gmt rename to dataset/20210517_voc.gmt index 1fc4a9ce52243fda8ec2b62c12494ff4b6821dba..734ac22771485bcd7d0409b154d995f26a1cf0bb 100644 --- a/dataset/20210511_voc.gmt +++ b/dataset/20210517_voc.gmt @@ -1,8 +1,8 @@ B.1.1.7 B.1.1.7 MN908947_Ampliseq:3208-3218 MN908947_Ampliseq:5329-5339 MN908947_Ampliseq:6895-6905 MN908947_Ampliseq:11228-11247 MN908947_Ampliseq:21705-21721 MN908947_Ampliseq:21931-21944 MN908947_Ampliseq:23004-23014 MN908947_Ampliseq:23212-23222 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:23545-23555 MN908947_Ampliseq:23650-23660 MN908947_Ampliseq:24447-24457 MN908947_Ampliseq:24855-24865 MN908947_Ampliseq:27913-27923 MN908947_Ampliseq:27989-27999 MN908947_Ampliseq:28052-28062 MN908947_Ampliseq:28221-28231 MN908947_Ampliseq:28222-28232 MN908947_Ampliseq:28223-28233 MN908947_Ampliseq:28918-28928 -B.1.351 B.1.351 MN908947_Ampliseq:1000-1010 MN908947_Ampliseq:5171-5181 MN908947_Ampliseq:10264-10274 MN908947_Ampliseq:11228-11247 MN908947_Ampliseq:21742-21752 MN908947_Ampliseq:22147-22157 MN908947_Ampliseq:22754-22764 MN908947_Ampliseq:22953-22963 MN908947_Ampliseq:23004-23014 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:23605-23615 MN908947_Ampliseq:25504-25514 MN908947_Ampliseq:25845-25855 MN908947_Ampliseq:26397-26407 MN908947_Ampliseq:28828-28838 MN908947_Ampliseq:23344-23354 +B.1.351 B.1.351 MN908947_Ampliseq:1000-1010 MN908947_Ampliseq:5171-5181 MN908947_Ampliseq:10264-10274 MN908947_Ampliseq:11228-11247 MN908947_Ampliseq:21742-21752 MN908947_Ampliseq:22147-22157 MN908947_Ampliseq:22754-22764 MN908947_Ampliseq:22953-22963 MN908947_Ampliseq:23004-23014 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:23605-23615 MN908947_Ampliseq:25504-25514 MN908947_Ampliseq:25845-25855 MN908947_Ampliseq:26397-26407 MN908947_Ampliseq:28828-28838 P.1 P.1 MN908947_Ampliseq:3769-3779 MN908947_Ampliseq:5589-5599 MN908947_Ampliseq:11228-11247 MN908947_Ampliseq:17200-17210 MN908947_Ampliseq:21555-21565 MN908947_Ampliseq:21562-21572 MN908947_Ampliseq:21579-21589 MN908947_Ampliseq:21915-21925 MN908947_Ampliseq:22073-22083 MN908947_Ampliseq:22753-22763 MN908947_Ampliseq:22953-22963 MN908947_Ampliseq:23004-23014 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:23466-23476 MN908947_Ampliseq:24583-24593 MN908947_Ampliseq:28108-28118 MN908947_Ampliseq:28210-28220 MN908947_Ampliseq:28453-28463 A.23.1 A.23.1 MN908947_Ampliseq:11171-11181 MN908947_Ampliseq:11207-11217 MN908947_Ampliseq:21808-21818 MN908947_Ampliseq:21974-21984 MN908947_Ampliseq:22602-22612 MN908947_Ampliseq:23342-23352 MN908947_Ampliseq:23545-23555 MN908947_Ampliseq:28085-28095 MN908947_Ampliseq:28108-28118 MN908947_Ampliseq:28819-28829 MN908947_Ampliseq:29468-29478 -B.1.525 B.1.525 MN908947_Ampliseq:14348-14358 MN908947_Ampliseq:11228-11247 MN908947_Ampliseq:21705-21721 MN908947_Ampliseq:21658-21668 MN908947_Ampliseq:22953-22963 MN908947_Ampliseq:23534-23544 MN908947_Ampliseq:24165-24175 MN908947_Ampliseq:26246-26256 MN908947_Ampliseq:26708-26718 MN908947_Ampliseq:28218-28231 +B.1.525 B.1.525 MN908947_Ampliseq:14348-14358 MN908947_Ampliseq:11228-11247 MN908947_Ampliseq:21705-21721 MN908947_Ampliseq:21658-21668 MN908947_Ampliseq:22953-22963 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:23534-23544 MN908947_Ampliseq:24165-24175 MN908947_Ampliseq:26246-26256 MN908947_Ampliseq:26708-26718 MN908947_Ampliseq:28218-28231 B.1.427 B.1.427 MN908947_Ampliseq:1000-1010 MN908947_Ampliseq:9679-9689 MN908947_Ampliseq:14349-14359 MN908947_Ampliseq:16335-16345 MN908947_Ampliseq:16955-16965 MN908947_Ampliseq:21541-21551 MN908947_Ampliseq:21959-21969 MN908947_Ampliseq:22858-22868 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:25504-25514 MN908947_Ampliseq:28828-28838 B.1.429 B.1.429 MN908947_Ampliseq:1000-1010 MN908947_Ampliseq:12819-12829 MN908947_Ampliseq:14349-14359 MN908947_Ampliseq:16955-16965 MN908947_Ampliseq:21541-21551 MN908947_Ampliseq:21959-21969 MN908947_Ampliseq:22858-22868 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:25504-25514 MN908947_Ampliseq:28828-28838 B.1.616 B.1.616 MN908947_Ampliseq:1000-1010 MN908947_Ampliseq:4177-4187 MN908947_Ampliseq:5119-5129 MN908947_Ampliseq:6988-6998 MN908947_Ampliseq:9684-9694 MN908947_Ampliseq:11024-11034 MN908947_Ampliseq:14349-14359 MN908947_Ampliseq:15846-15856 MN908947_Ampliseq:18449-18459 MN908947_Ampliseq:21018-21028 MN908947_Ampliseq:21429-21439 MN908947_Ampliseq:21699-21709 MN908947_Ampliseq:21928-21938 MN908947_Ampliseq:21931-21944 MN908947_Ampliseq:22147-22157 MN908947_Ampliseq:22951-22961 MN908947_Ampliseq:23344-23354 MN908947_Ampliseq:23466-23476 MN908947_Ampliseq:23508-23518 MN908947_Ampliseq:24349-24359 MN908947_Ampliseq:25062-25072 MN908947_Ampliseq:25504-25514 MN908947_Ampliseq:26245-26255 MN908947_Ampliseq:26273-26283 MN908947_Ampliseq:26836-26846 MN908947_Ampliseq:27207-27246 MN908947_Ampliseq:27698-27708 MN908947_Ampliseq:28238-28248 diff --git a/dataset/20210511_voc.txt b/dataset/20210517_voc.txt similarity index 99% rename from dataset/20210511_voc.txt rename to dataset/20210517_voc.txt index f19a3039e26bfba3a44ebef8cf96a2a20671ecbd..4ece6d4f2ed1c492a419308711e8c31a08969b40 100644 --- a/dataset/20210511_voc.txt +++ b/dataset/20210517_voc.txt @@ -69,7 +69,7 @@ B.1.525 MN908947_Ampliseq 11233 GTCTGGTTTT G ORF1ab:SGF_3675-3677_del B.1.525 MN908947_Ampliseq 21710 ATACATG A S:HV_69-70_del B.1.525 MN908947_Ampliseq 21663 A G S:Q52R B.1.525 MN908947_Ampliseq 22958 G A S:E484K -B.1.351 MN908947_Ampliseq 23349 A G S:D614G +B.1.525 MN908947_Ampliseq 23349 A G S:D614G B.1.525 MN908947_Ampliseq 23539 G C S:Q677H B.1.525 MN908947_Ampliseq 24170 T C S:F888L B.1.525 MN908947_Ampliseq 26251 C T E:L21F diff --git a/dev/convert.voc_gatk_2_gmt.R b/dev/convert.voc_gatk_2_gmt.R index d83ba09ba205a379a6c03de202c187b08309e0f7..dd7afcce897960402d3b331579f85b60a08d4360 100644 --- a/dev/convert.voc_gatk_2_gmt.R +++ b/dev/convert.voc_gatk_2_gmt.R @@ -12,7 +12,7 @@ rm(list = ls()) -date <- "20210511" +date <- "20210517" expanse <- 5 file.in <- "_voc.txt" file.out <- "_voc.gmt"